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Figure  S1. Fraction of genes expressed in different organs. Nod4-28, are nodules 4-28 days post-inoculation; Root 0 represents roots immediately prior to inoculation; Seed10-36 are seeds 10-36 days after pollination.

Figure  S2. Heat map of organ-induced genes. Transcripts levels for each of these genes were at least twice as high in one organ as in any other organ. The color scale shows log2-transformed transcript levels for each gene. Legume-specific genes (LSG) are indicated in the far-right column. Nod4-28 are nodules 4-28 days post-inoculation; Root0 represents roots immediately prior to inoculation; Seed10-36 are seeds 10–36 days after pollination.

Figure  S3. Transcriptional dynamics during nodule development of genes encoding enzymes involved in: (a) glycolysis; (b) carbon fixation; (c) nitrogen metabolism; and (d) flavonoid biosynthesis. Images were generated using MAPMAN v.2.0.2 software and values are shown as log2-transformed nodule/root transcript ratio. Images and mapping files can be downloaded at http://bioinfoserver.rsbs.anu.edu.au/utils/GeneBins/download.php and a file of the nodule time course data that can be downloaded into MAPMAN is provided as Table S6. Gene induction is shown in red and repression in blue.

Table  S1. List of organ-specific genes and their presence calls in all organs.

Table  S2. List of organ-induced genes and their transcript levels in all organs.

Table  S3. Differentially-expressed genes in Medicago. The table contains all genes that are expressed at a significantly different level in any organ compared to roots (P < 1.14 × 10−6).

Table  S4. Stably-expressed ‘reference’ genes for transcript normalization in Medicago. Probe sets with expression levels higher than 100 units showing coefficient of variation (CV) <16% among samples were selected. Low M-values from geNorm v.3.4 software (Vandesompele et  al., 2002) also indicate transcriptional stability among samples.

Table  S5. Genes differentially-expressed during nodule development. Only genes that were induced or repressed at least twofold compared with roots (P < 1.14 × 10−6) are included.

Table  S6. Nodule developmental data for visualization with MAPMAN software. Values are log2 (nodule/root transcript ratio).

Table  S7. Differential expression of TF genes in various organs of Medicago.

Table  S8. Legume specific genes and their expression level in different organs.

Table  S9. This table provides information about the various blast hits (better than 1 × 10−30 and bit-scores of 150) as well the sequences present in the AffyTrees phylogenies and the corresponding Pearson (linear) correlation of the expression values. These data are provided for the 10243 Medicago query sequences used to generate Figure 6. The values for the blast entries are: Arabidopsis gene-identifier; E-value; score; correlation coefficient. The values for the AffyTrees entries are: Arabidopsis gene-identifier; predicted as ortholog or homolog; correlation coefficient.

Please note: Blackwell Publishing are not responsible for the content or functionality of any supplementary materials supplied by the authors. Any queries (other than missing material) should be directed to the corresponding author for the article.

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TPJ_3519_sm_FigS1.pdf12KSupporting info item
TPJ_3519_sm_FigS2.tif448KSupporting info item
TPJ_3519_sm_FigS3.pdf5638KSupporting info item
TPJ_3519_sm_table1.xls1559KSupporting info item
TPJ_3519_sm_table2.xls8783KSupporting info item
TPJ_3519_sm_table3.xls19937KSupporting info item
TPJ_3519_sm_table4.xls5473KSupporting info item
TPJ_3519_sm_table5.xls10467KSupporting info item
TPJ_3519_sm_table6.xls1898KSupporting info item
TPJ_3519_sm_table7.xls1537KSupporting info item
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Please note: Wiley Blackwell is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.